What does the brown tint to email messages stored in a mailbox list mean?

Thanks for spending so much time on this. I did check for erroneous rules both in Mail Preferences and OS Preferences, but there were no rules (I didn't think there were because I didn't write any). I called support and they logged on, saw the problem, and then went to all the places where a switch could have done this. However, all was copasetic. The support tech finally had me go the [Format] menu and select white for the message color. It turned white, I then shut down mail and restarted it. The selected message was still there and its color was now normal. We tried this on several other messages and it proved to do the trick, and place the saved message back in the "normal" column. Again, thanks for your help. I do not know exactly when this problem started, but it was after (sometime after) I updated to El Capitan that I noticed it. Did NOT notice it under any previous OS.

[Personal Information Edited by Moderator]

Sorry, that's not the case. When selecting a junk email message by clicking and highlighting the message, the [JUNK] button in the toolbar changes to [NOT JUNK]. When selecting these "brown" tint messages, this does NOT happen. And the right click contextual menu does NOT list "Not Junk" but DOES list "Move To Junk". So, it's a good bet that the Mac Mail app does NOT think the selected message is junk. This is, of course, an attribute attached to the "metadata" for that message.